[2024-01-24 13:31:33,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference
[2024-01-24 13:31:34,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,895] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,895] [INFO] Running command: gunzip -c /var/lib/cwl/stgf03a1add-ba46-452e-bf41-58d112e7036e/GCF_014845115.1_ASM1484511v1_genomic.fna.gz | prodigal -d GCF_014845115.1_ASM1484511v1_genomic.fna/cds.fna -a GCF_014845115.1_ASM1484511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,472] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,472] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,472] [INFO] Running command: hmmsearch --tblout GCF_014845115.1_ASM1484511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference/reference_markers.hmm GCF_014845115.1_ASM1484511v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,784] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf03a1add-ba46-452e-bf41-58d112e7036e/GCF_014845115.1_ASM1484511v1_genomic.fna.gz]
[2024-01-24 13:31:48,829] [INFO] Query marker FASTA was written to GCF_014845115.1_ASM1484511v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,830] [INFO] Task started: Blastn
[2024-01-24 13:31:48,830] [INFO] Running command: blastn -query GCF_014845115.1_ASM1484511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference/reference_markers.fasta -out GCF_014845115.1_ASM1484511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,948] [INFO] Selected 9 target genomes.
[2024-01-24 13:31:49,948] [INFO] Target genome list was writen to GCF_014845115.1_ASM1484511v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,953] [INFO] Task started: fastANI
[2024-01-24 13:31:49,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgf03a1add-ba46-452e-bf41-58d112e7036e/GCF_014845115.1_ASM1484511v1_genomic.fna.gz --refList GCF_014845115.1_ASM1484511v1_genomic.fna/target_genomes.txt --output GCF_014845115.1_ASM1484511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:01,997] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:01,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:01,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:02,006] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:02,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:02,006] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Methylorubrum zatmanii	strain=LMG 6087	GCA_014845115.1	29429	29429	type	True	100.0	1551	1563	95	conclusive
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	87.8709	930	1563	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	87.7106	1231	1563	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	87.1063	1163	1563	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	87.0335	1135	1563	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	85.1082	1052	1563	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	84.4358	1012	1563	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	81.3145	695	1563	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	81.2731	734	1563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:02,008] [INFO] DFAST Taxonomy check result was written to GCF_014845115.1_ASM1484511v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:02,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:02,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:02,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference/checkm_data
[2024-01-24 13:32:02,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:02,065] [INFO] Task started: CheckM
[2024-01-24 13:32:02,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014845115.1_ASM1484511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014845115.1_ASM1484511v1_genomic.fna/checkm_input GCF_014845115.1_ASM1484511v1_genomic.fna/checkm_result
[2024-01-24 13:32:45,633] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:45,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,648] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:45,649] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:45,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014845115.1_ASM1484511v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:45,649] [INFO] Task started: Blastn
[2024-01-24 13:32:45,649] [INFO] Running command: blastn -query GCF_014845115.1_ASM1484511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg011c5407-cf88-483d-863f-aaeaba87ae1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014845115.1_ASM1484511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,742] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:47,742] [INFO] Target genome list was writen to GCF_014845115.1_ASM1484511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:47,748] [INFO] Task started: fastANI
[2024-01-24 13:32:47,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgf03a1add-ba46-452e-bf41-58d112e7036e/GCF_014845115.1_ASM1484511v1_genomic.fna.gz --refList GCF_014845115.1_ASM1484511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014845115.1_ASM1484511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:01,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:01,895] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:01,895] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014845115.1	s__Methylobacterium zatmanii	100.0	1551	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002355515.1	s__Methylobacterium populi_A	87.7563	1192	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138645.1	s__Methylobacterium thiocyanatum	87.7186	1170	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_014199985.1	s__Methylobacterium rhodesianum	87.711	1231	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.84	98.11	0.88	0.84	5	-
GCF_001423405.1	s__Methylobacterium sp001423405	87.2554	1117	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900234795.1	s__Methylobacterium extorquens	87.1025	1164	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.03	96.19	0.88	0.73	17	-
GCF_003201865.1	s__Methylobacterium sp003201865	87.0968	1089	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111705.1	s__Methylobacterium sp003111705	87.0298	1179	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.28	97.28	0.88	0.88	3	-
GCF_014191355.1	s__Methylobacterium sp014191355	86.8743	1126	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,897] [INFO] GTDB search result was written to GCF_014845115.1_ASM1484511v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:01,898] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:01,903] [INFO] DFAST_QC result json was written to GCF_014845115.1_ASM1484511v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:01,903] [INFO] DFAST_QC completed!
[2024-01-24 13:33:01,903] [INFO] Total running time: 0h1m29s